[English] 日本語
Yorodumi
- PDB-1tyt: CRYSTAL AND MOLECULAR STRUCTURE OF CRITHIDIA FASCICULATA TRYPANOT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tyt
TitleCRYSTAL AND MOLECULAR STRUCTURE OF CRITHIDIA FASCICULATA TRYPANOTHIONE REDUCTASE AT 2.6 ANGSTROMS RESOLUTION
ComponentsTRYPANOTHIONE REDUCTASE, OXIDIZED FORM
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Trypanothione reductase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsBailey, S. / Hunter, W.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structure of trypanothione reductase from Crithidia fasciculata at 2.6 A resolution; enzyme-NADP interactions at 2.8 A resolution.
Authors: Bailey, S. / Fairlamb, A.H. / Hunter, W.N.
#1: Journal: Eur.J.Biochem. / Year: 1993
Title: Substrate Interactions between Trypanothione Reductase and N1-Glutathionyldisulphide at 2.8 Angstroms Resolution
Authors: Bailey, S. / Smith, K. / Fairlamb, A.H. / Hunter, W.N.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Active Site of Trypanothione Reductase: A Target for Rational Drug Design
Authors: Hunter, W.N. / Bailey, S. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Aboagye-Kwarteng, T. / Smith, K. / Fairlamb, A.H.
#3: Journal: Mol.Microbiol. / Year: 1992
Title: Molecular Characterization of the Trypanothione Reductase Gene from Crithidia Fasciculata and Trypanosoma Brucei: Comparison with Other Flavo Protein Disulphide Oxidoreductases with Respect to ...Title: Molecular Characterization of the Trypanothione Reductase Gene from Crithidia Fasciculata and Trypanosoma Brucei: Comparison with Other Flavo Protein Disulphide Oxidoreductases with Respect to Substrate Specificity and Catalytic Mechanism
Authors: Aboagye-Kwarteng, T. / Smith, K. / Fairlamb, A.H.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: Initiating a Crystallographic Study of Trypanothione Reductase
Authors: Hunter, W.N. / Smith, K. / Derewenda, Z. / Harrop, S.J. / Habash, J. / Islam, M.S. / Helliwell, J.R. / Fairlamb, A.H.
History
DepositionJun 10, 1993Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPANOTHIONE REDUCTASE, OXIDIZED FORM
B: TRYPANOTHIONE REDUCTASE, OXIDIZED FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2974
Polymers105,7262
Non-polymers1,5712
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-78 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.800, 128.800, 92.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: CIS PROLINE - PRO A 43 / 2: CIS PROLINE - PRO A 370 / 3: CIS PROLINE - PRO A 462 / 4: CIS PROLINE - PRO B 43 / 5: CIS PROLINE - PRO B 370 / 6: CIS PROLINE - PRO B 462
DetailsTRYPANOTHIONE REDUCTASE IS ACTIVE AS A DIMER OF TWO IDENTICAL SUBUNITS, WHICH HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A AND B.

-
Components

#1: Protein TRYPANOTHIONE REDUCTASE, OXIDIZED FORM


Mass: 52862.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / References: UniProt: P39040, EC: 1.6.4.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS ONE DISCREPANCY BETWEEN THE CRYSTAL STRUCTURE AND THE AMINO ACID SEQUENCE DEDUCED FROM THE ...THERE IS ONE DISCREPANCY BETWEEN THE CRYSTAL STRUCTURE AND THE AMINO ACID SEQUENCE DEDUCED FROM THE GENE SEQUENCE. THIS IS AT POSITION 126. THE GENE SEQUENCE INDICATES A PHE, THE ELECTRON DENSITY MAPS SUGGEST A TRP.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal grow
*PLUS
Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mphosphate1drop
250 %satammonium sufate1drop
318 mg/mlprotein1drop
480 %satammonium sufate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 39038 / % possible obs: 83.5 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / Rfactor Rwork: 0.161 / Rfactor obs: 0.161 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7412 0 106 390 7908
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 35000 / Rfactor obs: 0.161 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.35
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_deg1.75

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more